Installation Error in Ubuntu 14.04

[shawnfahl]

Hello,

I keep receiving the following error while trying to install STAR:

d source && make STAR
make[1]: Entering directory /home/david/Documents/Software/STAR-2.5.1b/source' Makefile:91: Depend.list: No such file or directory make -C htslib lib-static make[2]: Entering directory/home/david/Documents/Software/STAR-2.5.1b/source/htslib'
cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c
In file included from bgzf.c:38:0:
htslib/bgzf.h:33:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^
compilation terminated.
make[2]: *** [bgzf.o] Error 1
make[2]: Leaving directory /home/david/Documents/Software/STAR-2.5.1b/source/htslib' make[1]: *** [htslib/libhts.a] Error 2 make[1]: Leaving directory/home/david/Documents/Software/STAR-2.5.1b/source'
make: *** [STAR] Error 2

Any help would be greatly appreciated. I have updated gcc and binutils, but I am still receiving this error.

Thanks.

Shawn

[alexdobin]

Hi @shawnfahl

it looks like you are missing zlib library, you would need to install it.

Cheers
Alex

[shawnfahl]

Hi Alex,

That was it. It works perfectly now.

Thanks so much!

Shawn

[benslack19]

Hello,
I know this is an old string but I seem to have a similar error even though I have zlib.h installed.

I ran make STAR from the source directory:
singlecell@lpt-hw0lzw1:~/bin/STAR-2.6.1a/source$ make STAR

But I get this returned:

Makefile:97: Depend.list: No such file or directory make -C htslib lib-static make[1]: Entering directory '/home/singlecell/bin/STAR-2.6.1a/source/htslib' cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c In file included from bgzf.c:38:0: htslib/bgzf.h:33:10: fatal error: zlib.h: No such file or directory #include <zlib.h> ^~~~~~~~ compilation terminated. Makefile:99: recipe for target 'bgzf.o' failed make[1]: *** [bgzf.o] Error 1 make[1]: Leaving directory '/home/singlecell/bin/STAR-2.6.1a/source/htslib' Makefile:107: recipe for target 'htslib/libhts.a' failed make: *** [htslib/libhts.a] Error 2

So I check to see if I have zlib.h:
singlecell@lpt-hw0lzw1:~/bin/STAR-2.6.1a/source$ whereis zlib.h
and it looks like I do:
zlib: /usr/include/zlib.h /usr/share/man/man3/zlib.3.gz

I tried running sudo apt-get install libz-dev but it indicated that I'm already running the latest version. Is there any assistance you can provide?

Thank you!
Ben

[alexdobin]

Hi Ben,

it looks like gcc cannot find zlib.h . Please check that /usr/include/ appears in the list of standard include directories with
$ gcc -xc -E -v -
$ gcc -xc++ -E -v -

Cheers
Alex

[benslack19]

Hi Alex, thanks for the reply and your help! I think I have this resolved now.

Best,
Ben

[DawnEve]

@benslack19 I have the same situation as you.
1.make error:
bgzf.h:33:10: fatal error: zlib.h: No such file or directory
2.$ whereis zlib.h
zlib: /usr/include/zlib.h /usr/share/man/man3/zlib.3.gz

I don't know how to include the file. Could you do me a faver.

Thank you,
George

[alexdobin]

Hi George,

this means you do not have the zlib library installed.

Instead of compiling, you can also try to use the pre-compiled executables in bin/

Cheers
Alex

[RaktimChowdhury]

(base) raktimbio@Raktim-Workstation:~/tools/STAR/source$ make STAR
make -C htslib lib-static
make[1]: Entering directory '/home/raktimbio/tools/STAR/source/htslib'
cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kfunc.o kfunc.c
cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o knetfile.o knetfile.c
cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kstring.o kstring.c
cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c
In file included from bgzf.c:38:
htslib/bgzf.h:33:10: fatal error: zlib.h: No such file or directory
33 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make[1]: *** [Makefile:99: bgzf.o] Error 1
make[1]: Leaving directory '/home/raktimbio/tools/STAR/source/htslib'
Makefile:137: Depend.list: No such file or directory
make: *** [Makefile:148: htslib/libhts.a] Error 2

I am getting the same problem. Can you please help me?? i am using WSL on WIN10.

[alexdobin]

Hi Raktim,

sorry for the belayed reply.
This error means that you need to install the zlib library.
I am not sure if it's possible to run STAR on WSL, the users who tried it before were not successful.

[RaktimChowdhury]

Hi Raktim,

sorry for the belayed reply. This error means that you need to install the zlib library. I am not sure if it's possible to run STAR on WSL, the users who tried it before were not successful.

Hello!!
I have tried to install STAR through conda environment in WSL and it works fine. Thank you.